Clostridium difficile is an epidemic infectious intestinal pathogen that usually infects patients with a compromised gut microbiome, and is currently treated with antibiotics with minimal success. Fecal Microbiota Transplantation is an emerging alternative therapy that shows promise: essentially, stool from a healthy donor is processed and administered to a patient, in order to restore healthy bacteria to the gut ecosystem. Our objective was to create a device to efficiently isolate, extract, and package viable microflora from donated stool efficiently, for administration to a patient or for further research.